Any possible to run cuffdiff without cuffqunt?

Question

[PK]

Hi folks, I have a doubt. Any possible to run cuffdiff without cuffqunt. In my point of view cuffqunt generated .cxb file. So we are taking .cxb file and merged.gtf files for cuffdiff input. My question is without .cxb file any possible to run cuffdiff. If it is available please help me.

[Rob]

Those two pieces of software are meant to be used together. Is there a particular reason you'd want to run cuffdiff without using the input that it is expecting from cuffquant?

[PK]

Thank you for your reply. No reasons but I want to know the difference between using cuffquant and not using cuffquand. does it make any impact on my output?

[igor]

It's just to speed things up:

Cuffquant allows you to compute the gene and transcript expression profiles and save these profiles to files that you can analyze later with Cuffdiff or Cuffnorm. This can help you distribute your computational load over a cluster and is recommended for analyses involving more than a handful of libraries.

http://cole-trapnell-lab.github.io/cufflinks/manual/

Answer 1

[igor]

As per Cuffdiff documentation, you can give it SAM/BAM/CXB files (only CXB are from Cuffquant):

Note that Cuffdiff can also accepted BAM files (which are binary, compressed SAM files). It can also accept CXB files produced by Cuffquant. Note that mixing SAM and BAM files is supported, but you cannot currently mix CXB and SAM/BAM. If one of the samples is supplied as a CXB file, all of the samples must be supplied as CXB files.

From http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/